Mercurial > repos > jowong > add_sample_as_first_line
comparison add_sample_name_as_first_line.py @ 0:231b21337c43 draft
planemo upload for repository https://github.com/jowong4/add_sample_name_as_first_line_of_file commit 462cf96a681fad46e20321feec5996d1e558a0d3
author | jowong |
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date | Thu, 27 Sep 2018 17:05:18 -0400 |
parents | |
children | 492848eff35d |
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-1:000000000000 | 0:231b21337c43 |
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1 import sys | |
2 import argparse | |
3 import re | |
4 | |
5 def Parser(): | |
6 the_parser = argparse.ArgumentParser(description="add sample name as first line of a tab file") | |
7 the_parser.add_argument('--input', required=True, action="store", type=str, help="input tab file") | |
8 the_parser.add_argument('--output', required=True, action="store", type=str, help="output file") | |
9 the_parser.add_argument('--sample', required=True, action="store", type=str, help="sample name to add as the first line of input file") | |
10 args = the_parser.parse_args() | |
11 return args | |
12 | |
13 args=Parser() | |
14 | |
15 sample_name = re.sub('[_12]*.fastq.gz', '', args.sample.rstrip().lstrip()) | |
16 | |
17 with open(args.input) as input: | |
18 with open(args.output, 'w') as output: | |
19 output.write(sample_name+"\n") | |
20 for line in input: | |
21 output.write(line) | |
22 | |
23 |